9LPK | pdb_00009lpk

Structure of human PADI6-UHRF1-UBE2D3 complex

• PDB DOI: https://doi.org/10.2210/pdb9LPK/pdb
• EM Map EMD-63270: EMDB EMDataResource

• Classification: LIGASE/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-25 Released: 2026-01-28 
• Deposition Author(s): Li, J., Deng, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

An essential maternal PADI6-UHRF1-UBE2D (MPU) complex regulates protein ubiquitination during oocyte maturation and embryogenesis

Li, J., Deng, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 368.92 kDa 
• Atom Count: 16,278 
• Modeled Residue Count: 2,069 
• Deposited Residue Count: 3,268 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A, F	793	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88  Go to UniProtKB:  Q96T88
PHAROS:  Q96T88 GTEx:  ENSG00000276043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-arginine deiminase type-6	B [auth C], C [auth B]	694	Homo sapiens	Mutation(s): 0  Gene Names: PADI6, PAD6 EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q6TGC4 (Homo sapiens) Explore Q6TGC4  Go to UniProtKB:  Q6TGC4
PHAROS:  Q6TGC4 GTEx:  ENSG00000276747

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	D [auth E], E [auth D]	147	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D3, UBC5C, UBCH5C EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P61077 (Homo sapiens) Explore P61077  Go to UniProtKB:  P61077
PHAROS:  P61077 GTEx:  ENSG00000109332

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Li, J., Deng, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31871449

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release